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This page was generated on 2024-03-28 11:40:07 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2031/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPLINTER 1.29.1  (landing page)
Diana Low
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/SPLINTER
git_branch: devel
git_last_commit: e51bf62
git_last_commit_date: 2024-03-27 09:16:28 -0400 (Wed, 27 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  YES
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

CHECK results for SPLINTER on lconway


To the developers/maintainers of the SPLINTER package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SPLINTER.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SPLINTER
Version: 1.29.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPLINTER_1.29.1.tar.gz
StartedAt: 2024-03-28 00:19:49 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 00:26:30 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 401.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SPLINTER.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPLINTER_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SPLINTER.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPLINTER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPLINTER’ version ‘1.29.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SPLINTER’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
eventPlot 13.966  0.293  14.389
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

SPLINTER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SPLINTER
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘SPLINTER’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SPLINTER)

Tests output


Example timings

SPLINTER.Rcheck/SPLINTER-Ex.timings

nameusersystemelapsed
acceptor.m0.0020.0020.004
addEnsemblAnnotation0.0050.0010.006
callPrimer30.0000.0000.001
checkPrimer0.0920.0040.097
compatible_cds0.0010.0010.002
compatible_tx0.0010.0010.002
donor.m0.0010.0010.002
eventOutcomeCompare1.6490.1001.766
eventOutcomeTranslate0.5320.0570.594
eventPlot13.966 0.29314.389
extendROI0.7110.0260.741
extractSpliceEvents0.0030.0010.005
extractSpliceSites0.0940.0070.101
findCompatibleEvents0.4170.0030.422
findCompatibleExon0.2260.0020.229
findTX0.0220.0010.023
getPCRsizes3.7530.2123.999
getRegionDNA0.3910.0250.421
insertRegion0.1950.0020.198
makeROI0.3290.0040.335
makeUniqueIDs0.0040.0010.005
pcr_result10.0010.0020.002
plot_seqlogo0.0470.0030.051
primers0.0000.0010.002
psiPlot0.2750.0160.294
region_minus_exon0.0010.0010.003
roi0.0010.0010.001
shapiroAcceptor0.5820.0360.626
shapiroDonor0.5660.0380.608
splice_data0.0010.0020.002
splice_fasta0.0010.0010.002
splitPCRhit0.0470.0020.049
thecds0.0000.0010.002
theexons0.0010.0020.002
valid_cds0.0000.0010.002
valid_tx0.0010.0010.002